From South Gilroy, the south end of the passenger
track on the west side, where a short stretch speed limited at 35 mph begins,
the line passes a bridge over drainage, a rail-served plant on the east side,
and the Caltrain (Joint Powers
Board) storage sidings are on the west side of the main line, south of the depot
at
Gilroy (MP 77.0), south end of Caltrain service, which is also on
the west side of the line with its platforms and platform tracks alongside the
line on the west side. The main line in this area is UP-owned single track CTC
with passing sidings, with maximum speeds of 79 mph for passenger trains and 60
mph for freights beginning north of the passenger tracks at Gilroy, as the
passenger track ends at North Gilroy, with the line
heads north-northwest, past four grade crossings in town.

The descending line passes extra track on the east side, a grade crossing, a
bridge over drainage, a grade crossing, a bridge over drainage, a grade
crossing, a dirt road grade crossing, a rail-served cement plant on the east
side, Intermediate Signals at MP 74.6 and a grade crossing at Rucker (MP 74.0), three grade
crossings, a rail-served plant on the east side, and a passenger station (west
side platform and shelter only) at San Martin (MP 71.2), with a road alongside
to the west. The line edges a bit more to the westward of
north, past a bridge over a stream, a 10,529 ft. east side siding at Morgan Hill (MP 70.1 to 68.1),
a road alongside to the east, a grade crossing, a spur trailing in on the east
side, a grade crossing, a passenger station (east side platform, parking to the
east; both sides by June, 2013)
at Morgan Hill (JPBX) at MP 67.5, a bridge over a road, a detector at MP 66.2, a
road alongside to the east, a grade crossing, Perry (MP 64.5), and
the start of two main tracks, CTC, at Coyote (MP 59.9). Monterey Road is
alongside to the east, with Coyote Creek Parkway (a protected area along the
eponymous creek) beyond it. The line curves northwest, past tract housing on the
west side of the line, Bernal Road and SR 85 bridging separately overhead, the passenger station,
with platform on the east side (both sides by June, 2013), at Blossom Hill (MP 55.7),
where Blossom Hill Road bridges overhead and Monterey Road becomes SR 82, and
Oak Grove. There are grade crossings at Chenoweth Avenue, Branham Lane and
Skyway Drive, with Intermediate Signals at MP 54.2 adjacent to one of them, a
detector at MP 52.6, Capitol Expressway bridges overhead, and there is a passenger station,
with platform on the east side (both sides by June, 2013), at Capitol (MP 52.4).

The line edges a bit further westward in direction, turning away from Monterey
Road, and JPB
ownership starts at CP Lick (MP 51.6), where the speed limit drops to 35 mph,
there are crossovers and an SP branch from Alamitos once trailed in from the
southwest. Curtner Avenue bridges overhead, as the line turns back to its former
northwest heading and the Guadalupe Freeway (SR 87) comes alongside to the west.
At Luther Junction (signals, MP 50.4),
a connecting track from some industrial spurs further east trails in from the
northeast. Almaden Expressway bridges overhead and Almaden Road passes below an
underbridge, and the erstwhile Western Pacific line around the south side of San
Jose crosses the line at CP Michael (MP 49.7). There are three north-facing
stub-end tracks on the west wide where the ACE trains lay over during the day, the line bridges over Alma Avenue, passing the Caltrain station at Tamien (MP 49.2),
with its platform and extra tracks on the west side of the line, which is
elevated above ground level at this point, and runs parallel to the San Jose
Light rail line just further west
(in the median of the Guadalupe Freeway).

There are crossovers at CP Mack (MP 49.2),
just north of Tamien station, where the passenger tracks trail in, a bridge over
Willow Street, the line
angles west, bridging across SR 87 as it does so, then bridges separately over
Prevost Street and Delmas Avenue, passes the crossovers at CP Delmas (MP 48.7),
bridges over Bird Avenue and I-280 as it turns northwest, and then turns north at the crossovers at CP Cahill (MP 47.7), where the speed
limit drops to 15 mph, there is a road bridge (San Carlos Street) overhead, the branch from Los Gatos trails in from the southwest,
and the now single (main) track line (with extra tracks on either side for the
station beginning immediately north of CP Cahill) runs across a bridge
over Park Avenue below to San Jose (Diridon) passenger
station at MP 47.5.

The substantial depot at San Jose is on the east side of the line,
with parking lot to its east (at Cahill Street) and bus stops to its northeast, and the station has
one platform on the east side and two island platforms with umbrella sheds
(expanded to four island platforms, by June 2013, built where the Caltrain
maintenance depot used to be),
connected by a passenger subway (which also connects to the VTA Light Rail
Station on the west side of the tracks), and serving five platform tracks, with
one storage track for complete
passenger trains adjacent to the station. The
line crosses on a bridge over The Alameda below (with light rail line in tunnel below that),
with the arena where the Sharks hockey team plays adjacent on the east side
north of the street. CP Julian,
immediately north of the station and at the same mile marker, with a large array
of signals on a signal bridge controlling the northbound exits from the station
platforms and yard tracks, is a wye
junction with the former SP Milpitas Line (now the UP Warm Springs subdivision),
which heads due east at this point. Three Main Tracks begin, as the line turns
northwest to the signal bridge at CP Stockton (MP 46.4), the northwest apex of the wye, where there
are crossovers. Caltrain's 6-track
locomotive and passenger car depot was once on the west side of the tracks,
with the locomotive maintenance shops beyond them, further to the south.

The San Jose (Lenzen Avenue) locomotive roundhouse was once located on the east side of the
tracks adjacent to the north leg of the wye, on the north side of the concrete
bridge over W. Julian Avenue below; the remaining stalls in this
roundhouse existed into the 2000s. There was also once a small yard located
here. The line crosses Lenzen Avenue within the wye and bridges over W. Taylor
Street at the north end of the wye. The new (by June, 2013) Caltrain 8-track
maintenance depot is on the west side of the line, here. There is a Caltrain station at College Park (MP 46.3), with depot on the
west side of the line, the Hedding Street and I-880 road bridges pass overhead, and the south connections into Newhall Yard are just
north of this location. The erstwhile Newhall Yard once lay on the northeast side of the line at
MP 45.6, extending north to CP Franklin (MP 45.3), where there are crossovers
between the two Caltrain tracks on the west side.
There is a Caltrain station at Santa Clara (MP 44.9), with its depot on the west
side of the tracks, freight station to its south and parking lot to its north,
and southbound platform between the westernmost and center tracks. Santa Clara
Tower is still present, on the west side of the tracks north of the station, but
is out of use. The track carrying trains headed for or coming from Oakland is on
the far east side of the formation, in 2006. The three main tracks reduce to two at CP Coast (MP 44.7),
where the Two Main Track ex-SP line up the East Bay to Oakland turns away to the north while the
Two Main Track Caltrain (JPB) line curves west-northwest.

From south of San Jose to either the Golden Gate or north of Richmond, the railroad is in an urban area, although some
of the line through the marshes and salt flats bordering the southern end of San
Francisco Bay seems quite far from built-up areas. At CP Coast, the Coast Starlight turns away from the Coast Route,
running through the aforementioned marshes and salt flats to Newark.